PhenotypeSimulator: Flexible Phenotype Simulation from Different Genetic and Noise
Models

Simulation is a critical part of method development and assessment
in quantitative genetics. 'PhenotypeSimulator' allows for the flexible
simulation of phenotypes under different models, including genetic variant
and infinitesimal genetic effects (reflecting population structure) as well
as non-genetic covariate effects, observational noise and additional
correlation effects. The different phenotype components are combined into a
final phenotype while controlling for the proportion of variance explained
by each of the components. For each effect component, the number of
variables, their distribution and the design of their effect across traits
can be customised. For the simulation of the genetic effects, external
genotype data from a number of standard software ('plink', 'hapgen2'/
'impute2', 'genome', 'bimbam', simple text files) can be imported. The final
simulated phenotypes and its components can be automatically saved into .rds
or .csv files. In addition, they can be saved in formats compatible with
commonly used genetic association software ('gemma', 'bimbam', 'plink',
'snptest', 'LiMMBo').